A major program in the mass spectrometry laboratory a NIEHS is the application of tandem mass spectrometric techniques (MS/MS) to the structure elucidation of compounds of interest in the environmental health sciences. The structure determination of these compounds is basic to understanding the interactions of compounds within the body, especially those due to altered metabolism and those arising through the interactions of xenobiotics and biomolecules. These techniques are important because samples of interest are often complex mixtures and because the ionization techniques applicable to these samples often provide little or no structural information. Our approach to the development of MS/MS techniques is twofold: structure elucidation and increasing the sensitivity of the technique. Current projects in the area of structure determination include: 1) determination of the location of substituents and double bonds in compounds within the arachidonic acid cascade under negative ion FAB/MS/MS conditions; 2) development of hybrid MS/MS techniques such as selected reaction monitoring for the analysis of polyhalogenated aromatic compounds such as chlorinated and brominated dibenzofurans and cibenzodioxins; 3) determination of the structure of macrolide antibiotics and the bacterial enzymatic deactivation products; 4) determination of the structures of unusual modified nucleosides whose concentration was found to be elevated in the urine of patients with AIDS; 5) structure determination of peptides expressed by flu-infected cells that are recognized by T-cells as indicative of infected cells (biological model systems for AIDS infected cell recognition). A major effort in increasing MS/MS sensitivity has been in the combination of high flux/low level introductory systems such as nanoscale packed LC and CZE. We have successfully lowered the MS/MS acquisition levels several orders of magnitude for a number of analyte types including protein digests, peptides, modified nucleosides, HETEs and leukotrienes.